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Articles 1 - 23 of 23
Full-Text Articles in Genomics
Investigating Cryptic Diversity In The Hawaiian Endemic Plant, Psychotria Mariniana (Rubiaceae), Uyen Thi Hoang Nguyen
Investigating Cryptic Diversity In The Hawaiian Endemic Plant, Psychotria Mariniana (Rubiaceae), Uyen Thi Hoang Nguyen
Master's Theses
Islands, with their isolation and steep environmental gradients, serve as natural laboratories for studying speciation. Molecular phylogenetic and population genetic methods utilizing Next-Generation Sequencing (NGS) have revolutionized our ability to document patterns of genetic divergence and diversity. Cryptic diversity, genetically distinct populations that were previously unrecognized as unique, and cryptic speciation, where divergent genetic populations may be deserving of status as unique species, have been observed in many taxa. The Hawaiian Islands provide an ideal setting for studying divergence and speciation due to their extreme isolation, known ages, and volcanic origin. Previous work has investigated the evolutionary relationships of the …
Population Structure And Connectivity Of Atlantic Nurse Sharks (Ginglymostoma Cirratum) In The Bahamas And Outlying Areas, Baylie A. Fadool
Population Structure And Connectivity Of Atlantic Nurse Sharks (Ginglymostoma Cirratum) In The Bahamas And Outlying Areas, Baylie A. Fadool
School of Natural Resources: Dissertations, Theses, and Student Research
Understanding animal ecosystem dynamics and behavior at the individual and population levels is essential for identifying life-history patterns and important areas for management and conservation. Marine fish species often face minimal geographic barriers to movement, but environmental (temperature, salinity, current) or intrinsic barriers (philopatry, site fidelity) can dictate gene flow. Atlantic nurse sharks (Ginglymostoma cirratum) are an International Union for Conservation of Nature (IUCN) listed ‘vulnerable’ species and present a unique opportunity to investigate patterns of population structure and connectivity in large-bodied sharks. They are benthic and display reproductive philopatry, with recent work suggesting they have the capacity …
Population Structure Analysis Of Four Basal Higher-Attines Using Bioinformatic Approaches, Gabriel Mcdanield
Population Structure Analysis Of Four Basal Higher-Attines Using Bioinformatic Approaches, Gabriel Mcdanield
Biology Theses
Metapopulations within the family Formicidae are unique among other animals due to the large colonies they build, and the mating strategies required to fertilize a specialized reproductive caste that will often produce young for the life of the colony. One group of ants, the fungus-gardeners (tribe Attini). The population structure of North American non-leafcutting, fungus-gardening ants has been understudied, especially in the southwest of the United States. Additionally, not much is known about their dispersal biology, so the dynamics of dispersal of these species and how they affect population structure is likewise not well known. To shed light on the …
Genomic Structure Among Populations Of A Regionally Rare Perennial Plant Indicates The Need For Reevaluation Of Management Units, Cheyenne Moore, Angela J. Mcdonnell, Scott Schuette, Christopher T. Martine
Genomic Structure Among Populations Of A Regionally Rare Perennial Plant Indicates The Need For Reevaluation Of Management Units, Cheyenne Moore, Angela J. Mcdonnell, Scott Schuette, Christopher T. Martine
Faculty Journal Articles
Conservation of rare species often relies on the delineation of management units and genomic tools can now be applied for this purpose. However, this is not as common on a local scale, where populations are often small and fragmented, despite the utility of informing conservation and management practice at the regional level. We use a genotyping by sequencing (GBS) approach to assess the perennial riparian plant species Baptisia australis (Fabaceae) in Pennsylvania, where the taxon is at the edge of its natural distribution and considered threatened. In this system, we investigate whether sampled subpopulations exhibit genetic structure. We find that …
The Influence Of Environmental Change On Genetic Diversity Across Spatial And Taxonomic Scales, Connor M. French
The Influence Of Environmental Change On Genetic Diversity Across Spatial And Taxonomic Scales, Connor M. French
Dissertations, Theses, and Capstone Projects
The spatial distribution of genetic diversity is of interest to biodiversity scientists and conservationists and is a fundamental metric of biodiversity. Genetic diversity patterns across spatial and taxonomic scales contain information about population and assemblage dynamics that can convey their resilience to environmental change. Ectotherms are especially linked to their environments and may be especially sensitive to fluctuations in the environment over time. Herein, I investigate global and regional patterns of genetic diversity in two groups of ectotherms, insects and lizards, to understand the relationship between environmental change and genetic diversity, from populations to assemblages. Overall, my research aims to …
Omani Camels From A Cultural And Genomics Perspective, Al Muatasim Al Zadjali
Omani Camels From A Cultural And Genomics Perspective, Al Muatasim Al Zadjali
Electronic Theses and Dissertations
The Dromedarian camel, Camelus dromedarius, is native to the Arabian Peninsula, including the Sultanate of Oman. These camels are used for food, milk, as well as show and racing competitions. Despite their economic and cultural importance research on camels in Oman is limited. The goal of this study was to examine their genomic variation, relationship with camels in other parts of the Arabian Peninsula, and to determine if selective breeding has led to the establishment of distinct breeds in Oman. Information was compiled from multiple sources to produce a comprehensive review on the breeding, management, economic and cultural use, …
Characterization Of The Immunoglobulin Lambda Chain Across Diverse Human Populations., William Gibson
Characterization Of The Immunoglobulin Lambda Chain Across Diverse Human Populations., William Gibson
Electronic Theses and Dissertations
The adaptive immune system relies on a diverse set of over one hundred immunoglobulin (IG) genes across three genomic loci that are variably combined to form antibodies (Ab). The IG Lambda locus is one of two loci which encodes the IG light chain. The complexity of the IGL locus severely limits the effective use of standard short-read sequencing, limiting our knowledge of population diversity in these loci. We leveraged single molecule real-time (SMRT) long-read sequencing in conjunction with IGL-targeted DNA capture to develop the method IG-Cap for accurate and high-throughput sequencing of the IGL locus. We benchmarked this method using …
A Comparison Of Microsatellites And Single Nucleotide Polymorphisms For The Assessment Of Population Structure In The Amblyomma Maculatum Koch, 1844 Species Complex, Henrey A. Deese
Electronic Theses and Dissertations
The Gulf Coast tick, Amblyomma maculatum Koch, 1844 is widespread throughout North and Central America and is the primary vector for the emerging pathogen Rickettsia parkeri. In the U.S., the population in the Southwest (A. maculatum morphotype III) is morphologically different from the population east of the Rocky Mountains (A. maculatum morphotype II). This research tests the hypothesis that A. maculatum morphotype II and morphotype III represent distinct species through the analysis and comparison of 6 microsatellite loci and suite of 135,221 Single nucleotide polymorphisms (SNPs) generated from ddRADseq. Population genetic analysis of both microsatellites and SNPs …
Plastic And Evolved Responses In The Eastern Oyster, Crassostrea Virginica, To Environmental Variation In The Northern Gulf Of Mexico, Kyle Sirovy
LSU Doctoral Dissertations
Climate change and other anthropogenic impacts are causing rapid alterations to many of the world’s most productive coastal ecosystems and there is an urgent need to understand how species will respond to these environmental changes. Organisms may respond through plasticity, evolution, or the evolution of plasticity. In this dissertation, I evaluate the role of plastic and evolved responses in the eastern oyster, Crassostrea virginica, to environmental variation in the northern Gulf of Mexico. I use comparative transcriptomics, physiology, and morphology to examine the relative contribution of plastic and evolved responses for oysters exposed to low salinity and outplant sites …
Evaluating Population Genetic Structure And Potential Genomic Signals Of Natural Selection In A Migratory Songbird (Protonotaria Citrea), Tyler A. Hohenstein
Evaluating Population Genetic Structure And Potential Genomic Signals Of Natural Selection In A Migratory Songbird (Protonotaria Citrea), Tyler A. Hohenstein
Theses and Dissertations
In this study I attempted to further resolve the population genetic structure in the Prothonotary Warbler (Protonotaria citrea), and conducted an outlier SNP analysis and exploratory gene ontology analysis to investigate potential ongoing natural selection in the species. This analysis of population structure confirms previous work by DeSaix et al. (2019), where weak population structure was observed between eastern sites along the Atlantic Coastal Plain, and western sites in the Mississippi Alluvial Valley, possibly due to a genetic discontinuity across the Appalachian Mountains. I conducted two forms of outlier SNP analyses, a principal component analysis (PCA)-based approach to identify SNPs …
Population Genomics Of Redbreast Sunfish (Lepomis Auritus): Exploring Gene Flow And Local Adaptation In A Widely Distributed Freshwater Fish, Garret J. Strickland
Population Genomics Of Redbreast Sunfish (Lepomis Auritus): Exploring Gene Flow And Local Adaptation In A Widely Distributed Freshwater Fish, Garret J. Strickland
College of Graduate Studies: Theses & Dissertations
Little information is available concerning the distribution of genetic diversity in non-salmonid, non-imperiled, freshwater fish. In order to fill in this knowledge gap, I conducted a population genomics survey in Redbreast Sunfish (Lepomis auritus; RBS), a widespread, generalist species distributed along the Atlantic slope rivers of eastern North America. I sampled four basins (ACF, Savannah, Roanoke, and James) at eight sites each with a factorial experimental design. Sites were distributed among coastal plain, Piedmont, or mountain ecoregions in order to capture the greatest range of environmental states experienced by RBS, with the intention of finding evidence for local adaptation to …
An Analysis Of The Spatial Genetic Structure Of A Hybrid Zone Between Two Species Of Killifish, Fundulus Heteroclitus And F. Grandis, Andrew Lee Hardy
An Analysis Of The Spatial Genetic Structure Of A Hybrid Zone Between Two Species Of Killifish, Fundulus Heteroclitus And F. Grandis, Andrew Lee Hardy
UNF Graduate Theses and Dissertations
Hybridization offers unique insight into the evolutionary process of speciation and the forces that maintain barriers to reproduction. In northeast Florida, a hybrid zone between two species of killifish, Fundulus heteroclitus and F. grandis, has been identified near Flagler Beach, FL, although the exact boundaries of the hybrid zone remain unknown (Gonzalez et al. 2009). This study aims to determine the fine-scale spatial genetic patterns of the hybrid zone and test the hypothesis that species ranges are influenced by changes in dominant vegetation. Results from an ADMIXTURE analysis and FST data indicated the boundary of the area of …
Comparative Conservation Genomics Of A Suite Of Imperiled Freshwater Mussels, Scott C. Meyer
Comparative Conservation Genomics Of A Suite Of Imperiled Freshwater Mussels, Scott C. Meyer
College of Graduate Studies: Theses & Dissertations
Maintenance of genetic diversity is a critical component to the management and recovery of imperiled species. By ensuring that a species’ genetic diversity is maintained, issues like inbreeding depression and loss of local adaptation can be prevented. However, the genetic diversity of many species are not well-characterized, and the factors that influence a species’ genetic diversity are often not well understood. In the case of imperiled unionid freshwater mussels, it is important to conduct conservation genetic assessments to aid in their management and preserve genetic diversity. This is the first study to conduct a comparative conservation genomic assessment for eight …
Lepidopteran Granivory Reduces Seed Counts In A Rare Species Of Riparian Scour Prairies, Cheyenne Moore, Angela J. Mcdonnell, Scott Schuette, Christopher T. Martine
Lepidopteran Granivory Reduces Seed Counts In A Rare Species Of Riparian Scour Prairies, Cheyenne Moore, Angela J. Mcdonnell, Scott Schuette, Christopher T. Martine
Faculty Journal Articles
In Pennsylvania Baptisia australis var. australis is found along only four waterways: the Allegheny River, Youghiogheny River, Clarion River, and Red Bank Creek. Because of its limited distribution and small number of extant populations, the species is considered state-threatened in Pennsylvania. In addition, the riparian prairie habitat that Pennsylvania Baptisia australis var. australis is restricted to is also in decline and considered vulnerable. Because of these conservation concerns, insights into the natural history of the taxon in the state is valuable and will inform conservation efforts. Field surveys and fruit collections along the Allegheny River and herbarium collections were used …
Investigation Into The Genetic Provenance Of Three Rare Plants With East-West Disjunction Patterns In Pennsylvania., Scott Schuette, Christopher T. Martine
Investigation Into The Genetic Provenance Of Three Rare Plants With East-West Disjunction Patterns In Pennsylvania., Scott Schuette, Christopher T. Martine
Other Faculty Research and Publications
Rare plant conservation relies on an understanding of the natural history, biology and ecology, and real and potential threats to their populations to inform state regulations that serve to protect the species from extirpation. This work often involves extensive field surveys over several years to determine population sizes and whether those populations are seeing reductions in number of individuals necessary to maintain the genetic diversity within and between those populations. Species and populations with high genetic diversity are better equipped to withstand sudden changes to their habitats that derive from land use changes and changing climate. There are a variety …
Population Structure Of A Federally Endangered Plant (Astragalus Jaegerianus Munz, Fabaceae) With Limited Range Using Microsatellites, Sueann Neal
Electronic Theses, Projects, and Dissertations
Studies on population genetics examine the relationship and effects of population structure, migration, gene flow and demographic history, and are therefore important in the conservation of endangered species. Astragalus jaegerianus, a critically federally endangered species found in a geographically restricted range is investigated to determine population structure and genetic variation. Previous research on A. jaegerianus focused on DNA sequence data for cpDNA and nrDNA showed no variation. Further research on A. jaegerianus utilizing AFLP’s on the whole genome indicated substantial gene diversity and population structure consistent with geographically widespread species. AFLP research is a cost-effective process to identify levels …
Evolutionary Linkage Of Mimetic And Non-Mimetic Color Traits In A Coral Snake Mimicry Complex, John D. Curlis Jr
Evolutionary Linkage Of Mimetic And Non-Mimetic Color Traits In A Coral Snake Mimicry Complex, John D. Curlis Jr
College of Graduate Studies: Theses & Dissertations
Color polymorphism in aposematic mimicry systems is a perplexing phenomenon for evolutionary biologists, as theoretically the benefits of converging on a model phenotype should constrain the evolution of phenotypic diversity in these systems (i.e., color polymorphism should not occur). Nevertheless, color polymorphism in mimicry systems is prevalent throughout many taxa. In some of these systems, the evolution of color polymorphism results in the existence of non-mimetic morphs, such as those that are cryptic. The case of ground snakes (Sonora semiannulata) is unique in that color polymorphism encompasses both mimetic and cryptic morphs, as well as individual mimetic and …
Development Of An In Silico Kir Genotyping Algorithm And Its Application To Population And Cancer Immunogenetic Analyses, Howard Rosoff
Development Of An In Silico Kir Genotyping Algorithm And Its Application To Population And Cancer Immunogenetic Analyses, Howard Rosoff
Dissertations and Theses (Open Access)
Gene content determination and variant calling in the complex KIR genomic region are useful for immune system function analysis, pathogenesis and disease risk factor elucidation, immunotherapy development, evolutionary investigations, and human migration modeling. Sequence-specific oligonucleotide and sequence-specific primer PCR methods are the de facto standards for KIR presence/absence identification, but the current platforms are unsuitable for SNP calling, impractical for KIR typing large cohorts of DNA samples, and inapplicable for typing repositories in which sequence data, but not cells or cell analytes, are available. Alternative typing methods, such as in silico sequence-based typing, can address the problems associated with amplicon-based …
Genome-Wide Differentiation In Closely Related Populations: The Roles Of Selection And Geographic Isolation, Rebecca Safran, Elizabeth Scordato, Matt Wilkins, Joanna K. Hubbard, B. R. Jenkins, Tomáš Albrecht, Samuel Flaxman, H. Karaardiç, Yoni Vortman, Arnon Lotem, Patrik Nosil, P. Pap, Sheng-Feng Shen, S.-F. Chan, T. L. Parchman, Nolan C. Kane
Genome-Wide Differentiation In Closely Related Populations: The Roles Of Selection And Geographic Isolation, Rebecca Safran, Elizabeth Scordato, Matt Wilkins, Joanna K. Hubbard, B. R. Jenkins, Tomáš Albrecht, Samuel Flaxman, H. Karaardiç, Yoni Vortman, Arnon Lotem, Patrik Nosil, P. Pap, Sheng-Feng Shen, S.-F. Chan, T. L. Parchman, Nolan C. Kane
School of Biological Sciences: Faculty Publications
Population divergence in geographic isolation is due to a combination of factors. Natural and sexual selection may be important in shaping patterns of population differentiation, a pattern referred to as “isolation by adaptation” (IBA). IBA can be complementary to the well-known pattern of “isolation by distance” (IBD), in which the divergence of closely related populations (via any evolutionary process) is associated with geographic isolation. The barn swallow Hirundo rustica complex comprises six closely related subspecies, where divergent sexual selection is associated with phenotypic differentiation among allopatric populations. To investigate the relative contributions of selection and geographic distance to genome-wide differentiation, …
A Gene-Based Association Method For Mapping Traits Using Reference Transcriptome Data, Eric R. Gamazon, Heather Wheeler, Kaanan P. Shah, Sahar V. Mozaffari, Keston Aquino-Michaels, Robert J. Carroll, Anne E. Eyler, Joshua C. Denny, Gtex Consortium, Dan L. Nicolae, Nancy J. Cox, Hae Kyung Im
A Gene-Based Association Method For Mapping Traits Using Reference Transcriptome Data, Eric R. Gamazon, Heather Wheeler, Kaanan P. Shah, Sahar V. Mozaffari, Keston Aquino-Michaels, Robert J. Carroll, Anne E. Eyler, Joshua C. Denny, Gtex Consortium, Dan L. Nicolae, Nancy J. Cox, Hae Kyung Im
Bioinformatics Faculty Publications
Genome-wide association studies (GWAS) have identified thousands of variants robustly associated with complex traits. However, the biological mechanisms underlying these associations are, in general, not well understood. We propose a gene-based association method called PrediXcan that directly tests the molecular mechanisms through which genetic variation affects phenotype. The approach estimates the component of gene expression determined by an individual’s genetic profile and correlates ‘imputed’ gene expression with the phenotype under investigation to identify genes involved in the etiology of the phenotype. Genetically regulated gene expression is estimated using whole-genome tissue-dependent prediction models trained with reference transcriptome data sets. PrediXcan enjoys …
Identification Of Whole Mitochondrial Genomes From Venezuela And Implications On Regional Phylogenies In South America, Esther J. Lee, D. Andrew Merriwether
Identification Of Whole Mitochondrial Genomes From Venezuela And Implications On Regional Phylogenies In South America, Esther J. Lee, D. Andrew Merriwether
Human Biology Open Access Pre-Prints
Recent studies have expanded and refined the founding haplogroups of the Americas using whole mitochondrial (mtDNA) genome analysis. In addition to pan-American lineages, a number of studies have identified specific variants that show higher frequencies in restricted geographical areas. In order to further characterize Native American maternal lineages and specifically examine local patterns within South America, we analyzed twelve maternally unrelated Yekuana whole mtDNA genomes from one village (Sharamaña) that include the four major Native American haplogroups A2, B2, C1, and D1. Our study proposes a reconfiguration of one subhaplogroup A2 (A2aa) that is specific to South America and identifies …
Fighting Microbial Drug Resistance: A Primer On The Role Of Evolutionary Biology In Public Health, Gabriel Perron, R. Inglis, Pleuni Pennings, Sarah Cobey
Fighting Microbial Drug Resistance: A Primer On The Role Of Evolutionary Biology In Public Health, Gabriel Perron, R. Inglis, Pleuni Pennings, Sarah Cobey
Biology Department Faculty Works
Although microbes have been evolving resistance to antimicrobials for millennia, the spread of resistance in pathogen populations calls for the development of new drugs and treatment strategies. We propose that successful, long-term resistance management requires a better understanding of how resistance evolves in the first place. This is an opportunity for evolutionary biologists to engage in public health, a collaboration that has substantial precedent. Resistance evolution has been an important tool for developing and testing evolutionary theory, especially theory related to the genetic basis of new traits and constraints on adaptation. The present era is no exception. The articles in …
High Connectivity In The Deepwater Snapper Pristipomoides Filamentosus (Lutjanidae) Across The Indo-Pacific With Isolation Of The Hawaiian Archipelago, Michelle R. Gaither, Shelley A. Jones, Christopher Kelley, Stephen J. Newman, Laurie Sorenson, Brian W. Bowen
High Connectivity In The Deepwater Snapper Pristipomoides Filamentosus (Lutjanidae) Across The Indo-Pacific With Isolation Of The Hawaiian Archipelago, Michelle R. Gaither, Shelley A. Jones, Christopher Kelley, Stephen J. Newman, Laurie Sorenson, Brian W. Bowen
Fisheries Research Articles
In the tropical Indo-Pacific, most phylogeographic studies have focused on the shallow-water taxa that inhabit reefs to approximately 30 m depth. Little is known about the large predatory fishes, primarily snappers (subfamily Etelinae) and groupers (subfamily Epinephelinae) that occur at 100–400 m. These long-lived, slow-growing species support fisheries across the Indo-Pacific, yet no comprehensive genetic surveys within this group have been conducted. Here we contribute the first range-wide survey of a deepwater Indo-Pacific snapper, Pristipomoides filamentosus, with special focus on Hawai'i. We applied mtDNA cytochrome b and 11 microsatellite loci to 26 samples (N = 1,222) collected across …